The recovery and utilization of vanadium from vanadium-bearing shale are significant because vanadium is an important strategic metal. This study explored a cleaner metal extraction method to recover vanadium from vanadium-bearing shale using a novel strain of mutated Bacillus mucilaginosus (B.M) for an enhanced bioleaching process. The highly efficient bioleaching bacterium B.M-0.2 was obtained by chemical mutation using hydroxylamine hydrochloride. The optimal conditions for vanadium extraction by the mutagenized bacteria were 0.5 g/L ammonium nitrate, 5 g/L sucrose, pH 7.5, ore particle size of less than 0.074 mm accounting for 92.34% of the total, and pulp density of 10 g/L. Under these conditions, the vanadium leaching efficiency of B.M-0.2 was 8.16% higher than that of the original bacteria after a bioleaching period of 30 days. The Organic acid test results also showed that the mutant B.M-0.2 had notably high acid production. The genome of the mutant B.M-0.2 was sequenced via polymerase chain reaction, which revealed clear changes. Through KEGG pathway analysis, pathways related to the proteins that were differentially expressed between the two were also revealed. The results showed that the B.M mutated chemically using hydroxylamine hydrochloride has great potential to improve the recovery of vanadium from vanadium-bearing shale.